Green sea turtle (Chelonia mydas) population history indicates important demographic changes near the mid-Pleistocene transition
The increased availability of genome sequences has provided remarkable advances in our understanding of the evolutionary history of non-model species. One important consideration in evolutionary studies is the role of demographic history in shaping contemporary levels and distribution of genetic variation. In green sea turtles (Chelonia mydas), a draft genome sequence has recently been made available, yet little is known regarding how past demographic events have shaped genomic variation in populations of this species. In this study, single nucleotide polymorphisms were identified in the green sea turtle’s genome and used to reconstruct past demographic events. It was found that this green sea turtle population, from the South China Sea, experienced a marked expansion ca. 0.8 million years ago near the mid-Pleistocene transition (MPT). Simulations revealed that the past demographic history can at least partially be explained by changes in population structure and gene flow; possibly associated with the climatic and geomagnetic events occurring since the MPT. The results demonstrate the importance in considering the effects of gene flow when reconstructing historical changes in population size and provide an extensive set of genomic resources for future evolutionary studies of green sea turtles.
We thank the Duke Shared Cluster Resource for providing the computational resources, and A. Ochoa and K. Lohmann for comments on earlier drafts of this manuscript. We also appreciate the comments and suggestions from the reviewers for improving the manuscript. This study was supported by a grant from the Air Force Office of Scientific Research (#FA9550-14-1-0208) to SJ.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
The article does not contain any experiments with animals performed by any of the authors.
All sequence data are available within the NCBI BioProject database (accession no. PRJNA104937), polymorphism data and simulation results are available in Pangaea (https://doi.pangaea.de/10.1594/PANGAEA.890759), and analysis code and computer scripts are available in GitHub (https://github.com/rfitak/GST_Demographic_History).
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